Targeted molecular dynamics domain selection question

From: Aditya Ranganathan (
Date: Thu Feb 28 2019 - 17:19:49 CST

Dear All,

I had a syntactical question regarding targeted molecular dynamics
simulations performed using NAMD. I`m working on a TMD simulation where I
want to bias my protein from state A to state B. The system has 58500
atoms, of which 3314 atoms belong to the protein. I label the beta column
of the protein atoms in both the input pdb file (stateA.pdb) and the TMD
pdb file (target structure) with 1. The beta for all non-protein atoms are
set to 0 in both these pdb files. I only want to apply the harmonic
restraints to the protein alone and not any other atom in the system. The
output file for this trajectory reads as follows:

"Info: TMD domain 0 has 55159 atoms 55159 fitted 55159 biased
Info: TMD domain 1 has 3341 atoms 3341 fitted 3341 biased
Info: 58500 TMD ATOMS

TCL: Running for 30000000 steps
TMD 0 Domain: 0 58.2916 58.2916
TMD 0 Domain: 1 58.2916 6.8374
Since the output reads 58500 TMD atoms, I want to clarify if the TMD is
being performed on both the solvent and the protein here? Some of the
literature on the semantics is a little unclear.



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